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Evolutionary Genetics of Reptiles and Amphibians

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (30 September 2019) | Viewed by 60044

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Special Issue Editors

Prof. Dr. Sebastian Steinfartz

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Guest Editor

Institute of Biology, Molecular Evolution and Systematics of Animals, University of Leipzig, Leipzig, Germany
Interests: ecology; evolution; genetics

Prof. Dr. Jonathon Marshall

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Guest Editor

Department of Zoology, Weber State University, Ogden, UT, USA
Interests: species delimitation; evolutionary genetics

Dr. Katharina Wollenberg Valero

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Guest Editor

Department of Biological and Marine Sciences, University of Hull, Hull HU6 7RX, UK
Interests: evolutionary and functional genomics of climate stress and -adaptation

Special Issue Information

Dear Colleagues,

Despite being divided into two distinct taxonomic classes of vertebrates, amphibians and reptiles have been classically lumped together under the science of Herpetology due to their creeping and crawling movements. Indeed, both groups are fundamentally different regarding their general biology and environmental demands. Still, amphibian and reptile research has been integrated by the herpetological community in a very successful way, in which scientists often work in parallel on amphibian and reptile systems to address major scientific questions. During the 7th World Congress of Herpetology in Canada, we organised a symposium entitled “Speciation in amphibians and reptiles: from patterns to processes and mechanisms” to bring together leading herpetologists and integrate their research on crucial evolutionary topics. Since then, especially the field of Genomics has undergone a rapid expansion. With this Special Issue, we aim to summarize research on the evolutionary genetics of amphibians and reptiles. We invite studies that use genetic and genomic approaches to unravel basic questions of evolutionary biology on different taxonomic levels of amphibians and reptiles. Therefore, we invite submissions on speciation research, local adaptation, phenotypic plasticity, and also conservation-related issues, such as infectious diseases based in a detailed genetic or genomic framework. Manuscripts submitted to this Special Issue are guaranteed to have a quick and fair review process. Potential topics for the Special Issue include, but are not limited to:

Evolutionary systematics
Patterns and mechanisms of speciation
Local adaptation
Phenotypic plasticity and epigenetics
Gene expression
Genetics of emerging infectious diseases
Diversity and genetics of microbiota

We aim to reward the best paper published in the Special Issue with a publication fee waiver. Authors that would like to participate for this option should submit the following pre-submission material to one of the Guest Editors before 1 January 2019: a cover letter reasoning why their study is outstanding, an abstract, and a conceptual and methodological outline (not longer than one page) of the manuscript that will be submitted.

Dr. Sebastian Steinfartz
Prof. Dr. Jonathon Marshall
Dr. Katharina Wollenberg Valero
Guest Editors

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

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Keywords

herpetofauna
evolutionary genetics and genomics
systematics
speciation
adaptation
epigenetics
infectious diseases

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Published Papers (11 papers)

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14 pages, 1558 KiB

Open AccessArticle

The Role of Plasticity and Adaptation in the Incipient Speciation of a Fire Salamander Population

by Joana Sabino-Pinto, Daniel J. Goedbloed, Eugenia Sanchez, Till Czypionka, Arne W. Nolte and Sebastian Steinfartz

Genes 2019, 10(11), 875; https://doi.org/10.3390/genes10110875 - 31 Oct 2019

Cited by 8 | Viewed by 3706

Abstract

Phenotypic plasticity and local adaptation via genetic change are two major mechanisms of response to dynamic environmental conditions. These mechanisms are not mutually exclusive, since genetic change can establish similar phenotypes to plasticity. This connection between both mechanisms raises the question of how much of the variation observed between species or populations is plastic and how much of it is genetic. In this study, we used a structured population of fire salamanders (Salamandra salamandra), in which two subpopulations differ in terms of physiology, genetics, mate-, and habitat preferences. Our goal was to identify candidate genes for differential habitat adaptation in this system, and to explore the degree of plasticity compared to local adaptation. We therefore performed a reciprocal transfer experiment of stream- and pond-originated salamander larvae and analyzed changes in morphology and transcriptomic profile (using species-specific microarrays). We observed that stream- and pond-originated individuals diverge in morphology and gene expression. For instance, pond-originated larvae have larger gills, likely to cope with oxygen-poor ponds. When transferred to streams, pond-originated larvae showed a high degree of plasticity, resembling the morphology and gene expression of stream-originated larvae (reversion); however the same was not found for stream-originated larvae when transferred to ponds, where the expression of genes related to reduction-oxidation processes was increased, possibly to cope with environmental stress. The lack of symmetrical responses between transplanted animals highlights the fact that the adaptations are not fully plastic and that some level of local adaptation has already occurred in this population. This study illuminates the process by which phenotypic plasticity allows local adaptation to new environments and its potential role in the pathway of incipient speciation. Full article

(This article belongs to the Special Issue Evolutionary Genetics of Reptiles and Amphibians)

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13 pages, 1015 KiB

Open AccessArticle

Multi-Tissue Transcriptomes Yield Information on High-Altitude Adaptation and Sex-Determination in Scutiger cf. sikimmensis

by Sylvia Hofmann, Heiner Kuhl, Chitra Bahadur Baniya and Matthias Stöck

Genes 2019, 10(11), 873; https://doi.org/10.3390/genes10110873 - 31 Oct 2019

Cited by 3 | Viewed by 3760

Abstract

The Himalayas are one of earth’s hotspots of biodiversity. Among its many cryptic and undiscovered organisms, including vertebrates, this complex high-mountain ecosystem is expected to harbour many species with adaptations to life in high altitudes. However, modern evolutionary genomic studies in Himalayan vertebrates are still at the beginning. Moreover, in organisms, like most amphibians with relatively high DNA content, whole genome sequencing remains bioinformatically challenging and no complete nuclear genomes are available for Himalayan amphibians. Here, we present the first well-annotated multi-tissue transcriptome of a Greater Himalayan species, the lazy toad Scutiger cf. sikimmensis (Anura: Megophryidae). Applying Illumina NextSeq 500 RNAseq to six tissues, we obtained 41.32 Gb of sequences, assembled to ~111,000 unigenes, translating into 54362 known genes as annotated in seven functional databases. We tested 19 genes, known to play roles in anuran and reptile adaptation to high elevations, and potentially detected diversifying selection for two (TGS1, SENP5) in Scutiger. Of a list of 37 genes, we also identify 27 candidate genes for sex determination or sexual development, all of which providing the first such data for this non-model megophryid species. These transcriptomes will serve as a valuable resource for further studies on amphibian evolution in the Greater Himalaya as a biodiversity hotspot. Full article

(This article belongs to the Special Issue Evolutionary Genetics of Reptiles and Amphibians)

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14 pages, 1309 KiB

Open AccessArticle

Transcriptomic Signatures of Experimental Alkaloid Consumption in a Poison Frog

by Eugenia Sanchez, Ariel Rodríguez, Jose H. Grau, Stefan Lötters, Sven Künzel, Ralph A. Saporito, Eva Ringler, Stefan Schulz, Katharina C. Wollenberg Valero and Miguel Vences

Genes 2019, 10(10), 733; https://doi.org/10.3390/genes10100733 - 21 Sep 2019

Cited by 12 | Viewed by 5233

Abstract

In the anuran family Dendrobatidae, aposematic species obtain their toxic or unpalatable alkaloids from dietary sources, a process known as sequestering. To understand how toxicity evolved in this family, it is paramount to elucidate the pathways of alkaloid processing (absorption, metabolism, and sequestering). Here, we used an exploratory skin gene expression experiment in which captive-bred dendrobatids were fed alkaloids. Most of these experiments were performed with Dendrobates tinctorius, but some trials were performed with D. auratus, D. leucomelas and Allobates femoralis to explore whether other dendrobatids would show similar patterns of gene expression. We found a consistent pattern of up-regulation of genes related to muscle and mitochondrial processes, probably due to the lack of mutations related to alkaloid resistance in these species. Considering conserved pathways of drug metabolism in vertebrates, we hypothesize alkaloid degradation is a physiological mechanism of resistance, which was evidenced by a strong upregulation of the immune system in D. tinctorius, and of complement C2 across the four species sampled. Probably related to this strong immune response, we found several skin keratins downregulated, which might be linked to a reduction of the cornified layer of the epidermis. Although not conclusive, our results offer candidate genes and testable hypotheses to elucidate alkaloid processing in poison frogs. Full article

(This article belongs to the Special Issue Evolutionary Genetics of Reptiles and Amphibians)

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18 pages, 2907 KiB

Open AccessArticle

The Complete Mitochondrial Genome of Platysternon megacephalum peguense and Molecular Phylogenetic Analysis

by Hongdi Luo, Haijun Li, An Huang, Qingyong Ni, Yongfang Yao, Huailiang Xu, Bo Zeng, Ying Li, Zhimin Wei, Guohua Yu and Mingwang Zhang

Genes 2019, 10(7), 487; https://doi.org/10.3390/genes10070487 - 27 Jun 2019

Cited by 12 | Viewed by 4241

Abstract

Platysternon megacephalum is the only living representative species of Platysternidae and only three subspecies remain: P. m. megalorcephalum, P. m. shiui, and P. m. peguense. However, previous reports implied that P. m. peguense has distinct morphological and molecular features. The characterization of the mitogenome has been accepted as an efficient means of phylogenetic and evolutionary analysis. Hence, this study first determined the complete mitogenome of P. m. peguense with the aim to identify the structure and variability of the P. m. peguense mitogenome through comparative analysis. Furthermore, the phylogenetic relationship of the three subspecies was tested. Based on different tRNA gene loss and degeneration of these three subspecies, their rearrangement pathways have been inferred. Phylogenetic analysis showed that P. m. peguense is a sister group to (P. m. megalorcephalum and P. m. shiui). Furthermore, the divergence time estimation of these three subspecies coincided with the uplift of the Tibetan Plateau. This study shows that the genetic distances between P. m. peguense and the other two subspecies are comparable to interspecific genetic distances, for example within Mauremys. In general, this study provides new and meaningful insights into the evolution of the three Platysternidae subspecies. Full article

(This article belongs to the Special Issue Evolutionary Genetics of Reptiles and Amphibians)

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25 pages, 5163 KiB

Open AccessArticle

Mitochondrial Introgression, Color Pattern Variation, and Severe Demographic Bottlenecks in Three Species of Malagasy Poison Frogs, Genus Mantella

by Angelica Crottini, Pablo Orozco-terWengel, Falitiana C. E. Rabemananjara, J. Susanne Hauswaldt and Miguel Vences

Genes 2019, 10(4), 317; https://doi.org/10.3390/genes10040317 - 23 Apr 2019

Cited by 14 | Viewed by 5283

Abstract

Madagascar is a biodiversity hotspot particularly rich in amphibian diversity and only a few charismatic Malagasy amphibians have been investigated for their population-level differentiation. The Mantella madagascariensis group is composed of two rainforest and three swamp forest species of poison frogs. We first confirm the monophyly of this clade using DNA sequences of three nuclear and four mitochondrial genes, and subsequently investigate the population genetic differentiation and demography of the swamp forest species using one mitochondrial, two nuclear and a set of nine microsatellite markers. Our results confirm the occurrence of two main mitochondrial lineages, one dominated by Mantella aurantiaca (a grouping supported also by our microsatellite-based tree) and the other by Mantella crocea + Mantella milotympanum. These two main lineages probably reflect an older divergence in swamp Mantella. Widespread mitochondrial introgression suggests a fairly common occurrence of inter-lineage gene flow. However, nuclear admixture seems to play only a limited role in this group, and the analyses of the RAG-1 marker points to a predominant incomplete lineage sorting scenario between all five species of the group, which probably diverged relatively recently. Our demographic analyses show a common, severe and recent demographic contraction, inferred to be in temporal coincidence with the massive deforestation events that took place in the past 1000 years. Current data do not allow to conclusively delimit independent evolutionary units in these frogs, and we therefore refrain to suggest any taxonomic changes. Full article

(This article belongs to the Special Issue Evolutionary Genetics of Reptiles and Amphibians)

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16 pages, 2676 KiB

Open AccessArticle

Shedding Light on a Secretive Tertiary Urodelean Relict: Hynobiid Salamanders (Paradactylodon persicus s.l.) from Iran, Illuminated by Phylogeographic, Developmental, and Transcriptomic Data

by Matthias Stöck, Fatemeh Fakharzadeh, Heiner Kuhl, Beata Rozenblut-Kościsty, Sophie Leinweber, Riddhi Patel, Mehregan Ebrahimi, Sebastian Voitel, Josef Friedrich Schmidtler, Haji Gholi Kami, Maria Ogielska and Daniel W. Förster

Genes 2019, 10(4), 306; https://doi.org/10.3390/genes10040306 - 18 Apr 2019

Cited by 7 | Viewed by 5193

Abstract

The Hyrcanian Forests present a unique Tertiary relict ecosystem, covering the northern Elburz and Talysh Ranges (Iran, Azerbaijan), a poorly investigated, unique biodiversity hotspot with many cryptic species. Since the 1970s, two nominal species of Urodela, Hynobiidae, Batrachuperus (later: Paradactylodon) have been described: Paradactylodon persicus from northwestern and P. gorganensis from northeastern Iran. Although P. gorganensis has been involved in studies on phylogeny and development, there is little data on the phylogeography, systematics, and development of the genus throughout the Hyrcanian Forests; genome-wide resources have been entirely missing. Given the huge genome size of hynobiids, making whole genome sequencing hardly affordable, we aimed to publish the first transcriptomic resources for Paradactylodon from an embryo and a larva (9.17 Gb RNA sequences; assembled to 78,918 unigenes). We also listed 32 genes involved in vertebrate sexual development and sex determination. Photographic documentation of the development from egg sacs across several embryonal and larval stages until metamorphosis enabled, for the first time, comparison of the ontogeny with that of other hynobiids and new histological and transcriptomic insights into early gonads and timing of their differentiation. Transcriptomes from central Elburz, next-generation sequencing (NGS) libraries of archival DNA of topotypic P. persicus, and GenBank-sequences of eastern P. gorganensis allowed phylogenetic analysis with three mitochondrial genomes, supplemented by PCR-amplified mtDNA-fragments from 17 museum specimens, documenting <2% uncorrected intraspecific genetic distance. Our data suggest that these rare salamanders belong to a single species P. persicus s.l. Humankind has a great responsibility to protect this species and the unique biodiversity of the Hyrcanian Forest ecosystems. Full article

(This article belongs to the Special Issue Evolutionary Genetics of Reptiles and Amphibians)

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16 pages, 1900 KiB

Open AccessArticle

Evolutionary Insights of the ZW Sex Chromosomes in Snakes: A New Chapter Added by the Amazonian Puffing Snakes of the Genus Spilotes

by Patrik F. Viana, Tariq Ezaz, Marcelo de Bello Cioffi, Breno Jackson Almeida and Eliana Feldberg

Genes 2019, 10(4), 288; https://doi.org/10.3390/genes10040288 - 9 Apr 2019

Cited by 18 | Viewed by 5834

Abstract

Amazonian puffing snakes (Spilotes; Colubridae) are snakes widely distributed in the Neotropical region. However, chromosomal data are scarce in this group and, when available, are only limited to karyotype description using conventional staining. In this paper, we focused on the process of karyotype evolution and trends for sex chromosomes in two Amazonian Puffer Snakes (S. pulllatus and S. sulphureus). We performed an extensive karyotype characterization using conventional and molecular cytogenetic approaches. The karyotype of S. sulphureus (presented here for the first time) exhibits a 2n = 36, similar to that previously described in S. pullatus. Both species have highly differentiated ZZ/ZW sex chromosomes, where the W chromosome is highly heterochromatic in S. pullatus but euchromatic in S. sulphureus. Both W chromosomes are homologous between these species as revealed by cross-species comparative genomic hybridization, even with heterogeneous distributions of several repetitive sequences across their genomes, including on the Z and on the W chromosomes. Our study provides evidence that W chromosomes in these two species have shared ancestry. Full article

(This article belongs to the Special Issue Evolutionary Genetics of Reptiles and Amphibians)

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19 pages, 3075 KiB

Open AccessArticle

Satellite DNA Mapping in Pseudis fusca (Hylidae, Pseudinae) Provides New Insights into Sex Chromosome Evolution in Paradoxical Frogs

by Kaleb Pretto Gatto, Karin Regina Seger, Paulo Christiano de Anchieta Garcia and Luciana Bolsoni Lourenço

Genes 2019, 10(2), 160; https://doi.org/10.3390/genes10020160 - 19 Feb 2019

Cited by 8 | Viewed by 4446

Abstract

In the frog genus Pseudis, previous works found a sex-linked heteromorphism of the PcP190 satellite DNA in the nucleolus organizer region (NOR)-bearing chromosome pairs of Pseudis bolbodactyla and Pseudis tocantins, which possess a ZZ/ZW sex determination system. A pericentromeric inversion was inferred to have occurred during W chromosome evolution, moving a chromosomal cluster enriched by the PcP190 from the short arm (as observed in P. bolbodactyla) to the NOR-bearing long arm (as observed in P. tocantins). However, whether such an inversion happened in P. tocantins or in the common ancestor of Pseudis fusca and P. tocantins remained unclear. To assess this question, we mapped PcP190 in the karyotype of P. fusca from three distinct localities. Southern blotting was used to compare males and females. The mitochondrial H1 fragment (which contains the 12S ribosomal RNA (rRNA), tRNAval, and 16S rRNA genes) and cytochrome b gene were partially sequenced, and a species tree was inferred to guide our analysis. Pseudis fusca specimens were placed together as the sister group of P. tocantins, but based on genetic distance, one of the analyzed populations is probably an undescribed species. A cluster of PcP190, located in the long arm of chromosome 7, is sex linked in this putative new species but not in the remaining P. fusca. We could infer that the pericentromeric inversion that moved the PcP190 site to the NOR-bearing chromosome arm (long arm) occurred in the common ancestor of P. fusca, the putative undescribed species, and P. tocantins. Full article

(This article belongs to the Special Issue Evolutionary Genetics of Reptiles and Amphibians)

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47 pages, 4280 KiB

Open AccessReview

Patterns, Mechanisms and Genetics of Speciation in Reptiles and Amphibians

by Katharina C. Wollenberg Valero, Jonathon C. Marshall, Elizabeth Bastiaans, Adalgisa Caccone, Arley Camargo, Mariana Morando, Matthew L. Niemiller, Maciej Pabijan, Michael A. Russello, Barry Sinervo, Fernanda P. Werneck, Jack W. Sites, Jr., John J. Wiens and Sebastian Steinfartz

Genes 2019, 10(9), 646; https://doi.org/10.3390/genes10090646 - 26 Aug 2019

Cited by 42 | Viewed by 12058

Abstract

In this contribution, the aspects of reptile and amphibian speciation that emerged from research performed over the past decade are reviewed. First, this study assesses how patterns and processes of speciation depend on knowing the taxonomy of the group in question, and discuss how integrative taxonomy has contributed to speciation research in these groups. This study then reviews the research on different aspects of speciation in reptiles and amphibians, including biogeography and climatic niches, ecological speciation, the relationship between speciation rates and phenotypic traits, and genetics and genomics. Further, several case studies of speciation in reptiles and amphibians that exemplify many of these themes are discussed. These include studies of integrative taxonomy and biogeography in South American lizards, ecological speciation in European salamanders, speciation and phenotypic evolution in frogs and lizards. The final case study combines genomics and biogeography in tortoises. The field of amphibian and reptile speciation research has steadily moved forward from the assessment of geographic and ecological aspects, to incorporating other dimensions of speciation, such as genetic mechanisms and evolutionary forces. A higher degree of integration among all these dimensions emerges as a goal for future research. Full article

(This article belongs to the Special Issue Evolutionary Genetics of Reptiles and Amphibians)

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8 pages, 2056 KiB

Open AccessTechnical Note

Efficient Gene Disruption via Base Editing Induced Stop in Newt Pleurodeles waltl

by Hao Cai, Zhelun Peng, Ruimin Ren and Heng Wang

Genes 2019, 10(11), 837; https://doi.org/10.3390/genes10110837 - 23 Oct 2019

Cited by 8 | Viewed by 3538

Abstract

Loss-of-function approaches provide strong evidence for determining the role of particular genes. The prevalent CRISPR/Cas9 technique is widely used to disrupt target gene with uncontrolled non-homologous end joining after the double strand breaks, which results in mosaicism and multiple genotypes in the founders. In animal models with long generation time such as the salamanders, producing homozygous offspring mutants would be rather labor intensive and time consuming. Here we utilized the base editing technique to create the loss-of-function F0 mutants without the random indels. As a proof of principle, we successfully introduced premature stop codons into the tyrosinase locus and produced the albino phenotype in the newts (Pleurodeles waltl). We further demonstrated that the knockout efficiency could be greatly improved by using multiplex sgRNAs target the same gene. The F0 mutated animals showed fully loss-of-function by both genotyping and phenotyping analysis, which could enable direct functional analysis in the founders and avoid sophisticated breeding. This study not only presented the high efficiency of single base editing in a gigantic animal genome (>20 G), but also provided new tools for interrogating gene function in other salamander species. Full article

(This article belongs to the Special Issue Evolutionary Genetics of Reptiles and Amphibians)

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11 pages, 2074 KiB

Open AccessTechnical Note

Development and Validation of Sex-Specific Markers in Pelodiscus Sinensis Using Restriction Site-Associated DNA Sequencing

by Hongwei Liang, Lihua Wang, Hang Sha and Guiwei Zou

Genes 2019, 10(4), 302; https://doi.org/10.3390/genes10040302 - 15 Apr 2019

Cited by 20 | Viewed by 5148

Abstract

The sex of an animal influences its economic traits, especially in species displaying sexual dimorphism. The Chinese soft-shelled turtle, Pelodiscus sinensis, is an economically important aquatic species that shows significant male sexual dimorphism, with a large body size, faster growth, a thick and wide calipash, and lower body fat. In this study, ten male and ten female turtles were subjected to restriction site-associated DNA sequencing (RAD-seq) using the Hi-Seq 4000 sequencing platform to isolate female-specific DNA fragments. We identified 5967 bp and 6532 bp fragments using genome walking. Three female-specific markers designed from these two fragments were confirmed to separate the sexes of Pelodiscus sinensis perfectly. One of the female-specific markers showed dosage association in female and male individuals. Individuals from different populations (n = 296) were used to validate that the female-specific markers could identify the genetic sex of Pelodiscus sinensis with 100% accuracy. The results of the present study demonstrated that RAD-seq was useful to develop sex-related markers in animals, and verified that the sex determination system of Pelodiscus sinensis belonged to the ZZ/ZW heterogametic system. Importantly, the developed markers could lead to a method for sex-controlled breeding in the Chinese soft-shelled turtle. Full article

(This article belongs to the Special Issue Evolutionary Genetics of Reptiles and Amphibians)

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